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Automatic Behavior Recognition System (ABRS)
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ABRS_data_vis.py
ABRS_modules.py Update ABRS_modules.py Jun 5, 2019
ABRS_poster_SfN2016.pdf
ConvNet_training.ipynb
README.md
ST_features_to_etho_LDA.ipynb Add files via upload Jun 24, 2019
ST_image_to_ST_feature_batch.py
ST_images_samle_anterior.png
SampleImagesWingCleanin.png Add files via upload Jun 6, 2019
batch_3C_to_etho.ipynb
license.txt
modelConv2ABRS_3C
pcbi.1007105_1.pdf
real_time_ABRS.py
video_to_ST3C_image_batch.ipynb
video_to_ST_image_batch.py
visualize_ST3C_images.ipynb

README.md

Automatic Behavior Recognition System (ABRS)

Copyright (c) 2019 Primoz Ravbar UCSB Licensed under BSD 2-Clause [see LICENSE for details] Written by Primoz Ravbar

Automatic Behavior Recognition System can annotate behaviors of freely moving flies and possibly other animals from video. It does NOT require alignment of frames, segmentation, anatomical information nor pose estimation. It can reliably recognize behavior in highly variable backgrounds, animal orientations, positions, light levels, movie qualities and other conditions. It does that by extracting spatio-temporal features from video. These spatio-temporal features can then be used with supervised machine learning (ML) to classify behaviors.

The most current real-time version utilizes a small convolutional neural network directly from the video with simplified pre-processing. It can classify behavior in real-time. This version can be tested by cloning the ABRS and running real_time_ABRS. A sample model (the trained convolutional network) used is: modelConv2ABRS_3C Other, better models, can be found in the "Model" folder. That's it. It will produce an ethogram (record of behavior) from a video.

The pre-processing (production of ST-images) of video is crucial. It extracts features from raw video frames in three time-scales:

  1. Raw frame;
  2. Difference between two frames; and
  3. Spectral features extracted from a wider time window (typically .5 sec).

See ST_images_samle_anterior.png for an example of 3-channel spatio-temporal images (blue - raw frame; yellow/green - frame-to-frame difference; red - spectral features from broader time window). The fly in these images is involved in "leg rubbing" [1] and "head cleaning" behaviors [2]. The behavioral labels (classes) [1] and [2] above the images are automatically created by ABRS. Another example, SampleImagesWingCleanin.png, is showing several different flies, in various backgrounds, positions, orientations and light levels, all engaged in the same behavior (wing cleaning). Again, these highly variable images were classified as "wing cleaning" by the ABRS, illustrating good generalization.

ConvNet training is implemented by ConvNet_training.ipynb The trained CNN graph and weights can be used for the real-time and batch implementations. The training data consists of ST-images (3C) and labels.It will be uploaded shorty to Training Data folder.

The batch implementation (to read ST-images from multiple movies and produce ethograms) is batch_3C_to_etho.ipynb . This batch takes ST-images as the input and outputs ethograms.

A more direct batch implementation (to produce ST-images and predict behaviors directly from the movies) is: video_to_ST3C_image_batch.ipynb

The thoroughly tested older version is described below:

Also see the paper: Ravbar, Primoz, Kristin Branson, and Julie H. Simpson. "An automatic behavior recognition system classifies animal behaviors using movements and their temporal context." Journal of Neuroscience Methods (2019): 108352. (The whole paper will remain available to download for free until Oct 8, 2019 here: https://authors.elsevier.com/c/1Zb0pbXTOtIJC)

The extraction of the features is implemented in two steps: first, run video_to_ST_image_batch to produce "ST-images" (ST-images capture "shapes of movements" in a defined time-window), second, run ST_image_to_ST_feature_batch to reduce the dimensionality of the ST-images (to 30 spatio-temporal features - down from 80x80 = 6400 dimensions). Here the 30 dimensional spatio-temporal features ("STF") are stored in Data_demo/ST_features.

The STF files contain numpy matrices of the 30 spatio-temporal features calculated for every frame of the raw movies. They also contain max change of light intensity in the ST-image time-window and the total body displacement in the same window ("speed"). These features can be used in supervised or unsupervised ML steps. Here we provide an implementation based on LDA (supervised learning). The human labels are also provided.

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